VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Fri Apr 24 2009 - 08:42:34 CDT

On Thu, 2009-04-23 at 23:41 -0700, Gianluca Interlandi wrote:
> I am trying to solvate a protein using the solvate plugin of VMD. The PSF
> (X-PLOR format) and PDB were produced with CHARMM. I get the following
> error:
>
> vmd > solvate protein_xplor.psf protein.pdb -minmax {{-65 -65 -65} {65 65 65}}
> reading structure from psf file protein_xplor.psf
> Error processing bonds
>
> I'm using vmd version 1.8.6 on linux.
>
> I have uploaded the files here:
>
> http://artemide.bioeng.washington.edu/Files/protein_xplor.psf
>
> http://artemide.bioeng.washington.edu/Files/protein.pdb
>
>
> Any help would be appreciated.

try building a "normal" psf (w/o EXT). the readpsf command in psfgen
seems to be not yet updated for handling newer style .psf files.
work has been underway to interface psfgen to the molfile plugins,
some of which in turn have been improved to read in more fields
including angles and dihedrals. but as far as i can tell, it is not
completed yet. i just tried compiling that variant of psfgen from
the cvs and there are still some bugs. perhaps john knows more.

cheers,
   axel.

>
> Gianluca 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.